Biology subjects

Amsalem, O.

Publications and source records attributed to Amsalem, O..

16 recordsLinked to original sources

bioRxiv2026

EASI-PASS: An accessible pipeline for linking functional imaging and mRNA profiling

We developed EASI-PASS, a reliable, high-throughput method for estimating the molecular identity of functionally characterized cells by merging live imaging with subsequent fixed-tissue imaging using conventional microscopes. Our method matches the shapes and locations of thousands of densely imaged cells between large (>1 mm2) functional images and a thick, expanded, and cleared EASI-FISH tissue volume to assess gene expression. This approach is more efficient than alignment to thin sections and recovers the molecular identity of ~78% of cells. In acute brain slice imaging from the mouse parabrachial nucleus during optogenetic stimulation of long-range spinal inputs, we observed fine-scale specificity in the molecular identity of spinorecipient neurons. In the awake mouse visual cortex, we observed distinct arousal modulation and spatial falloff in correlations within and across interneuron classes. Thus, EASI-PASS provides reliable and efficient alignment of cellular activity with molecular identity.

neuroscience↗

bioRxiv2025

Brainstem sensing of multiple body signals during food consumption

Studies of body-to-brain communication often examine one stimulus or organ at a time, yet the brain must integrate many body signals during behavior. For example, food consumption generates diverse oral and post-oral chemical and mechanical signals transduced by well-characterized peripheral neuronal pathways. Far less is known about how these and other bodily signals are integrated and organized in the brainstem lateral parabrachial nucleus (LPBN), a key interoceptive sensory hub. We established methods to image the activity of 1000s of neurons throughout a large region of mouse LPBN. Food consumption drove a seconds-long wave of activity across LPBN, with dynamics mirroring the movement of food through the upper gastrointestinal tract observed using X-ray fluoroscopy. By imaging the same neurons across days, we found that spatially clustered subsets of neurons encoded oral signals, stomach filling, visceral malaise, arousal, and/or body movement. Moreover, only certain subsets were modulated by cortical input. Together, these experiments reveal a functional specialization in the LPBN that integrates contextual information from the body to guide behavior.

neuroscience↗

bioRxiv2025

Simultaneous, real-time tracking of many neuromodulatory signals with Multiplexed Optical Recording of Sensors on a micro-Endoscope

Dozens of extracellular molecules jointly impact a given neuron, yet we lack methods to simultaneously record many such signals in real time. We developed a probe to track ten or more neuropeptides and neuromodulators using spatial multiplexing of genetically encoded fluorescent sensors. Cultured cells expressing one sensor at a time are immobilized at the front of a gradient refractive index (GRIN) lens for 3D two-photon imaging in vitro and in vivo. The sensor identity and detection sensitivity of each cell are determined via robotic dipping of the probe into wells containing various ligands and concentrations. Using this probe, we detected stimulation-evoked release of multiple neuromodulators in acute brain slices. We also tracked endogenous and drug-evoked changes in cerebrospinal fluid composition in the awake mouse lateral ventricle, which triggered downstream activation of the choroid plexus epithelium. Our approach offers a first step towards quantitative, real-time, high-dimensional tracking of brain fluid composition.

neuroscience↗

bioRxiv2023

A spatial human thymus cell atlas mapped to a continuous tissue axis

T cells develop from circulating precursors, which enter the thymus and migrate throughout specialised sub-compartments to support maturation and selection. This process starts already in early fetal development and is highly active until the involution of the thymus in adolescence. To map the micro-anatomical underpinnings of this process in pre- vs. post-natal states, we undertook a spatially resolved analysis and established a new quantitative morphological framework for the thymus, the Cortico-Medullary Axis. Using this axis in conjunction with the curation of a multimodal single-cell, spatial transcriptomics and high-resolution multiplex imaging atlas, we show that canonical thymocyte trajectories and thymic epithelial cells are highly organised and fully established by post-conception week 12, pinpoint TEC progenitor states, find that TEC subsets and peripheral tissue genes are associated with Hassalls Corpuscles and uncover divergence in the pace and drivers of medullary entry between CD4 vs. CD8 T cell lineages. These findings are complemented with a holistic toolkit for spatial analysis and annotation, providing a basis for a detailed understanding of T lymphocyte development.

immunology↗

bioRxiv2023

A spatially-resolved transcriptional atlas of the murine dorsal pons at single-cell resolution

The "dorsal pons", or "dorsal pontine tegmentum" (dPnTg), is part of the brainstem. It is a complex, densely packed region whose nuclei are involved in regulating many vital functions. Notable among them are the parabrachial nucleus, the Kolliker Fuse, the Barrington nucleus, the locus coeruleus, and the dorsal, laterodorsal, and ventral tegmental nuclei. In this study, we applied single-nucleus RNA-seq (snRNA-seq) to resolve neuronal subtypes based on their unique transcriptional profiles and then used multiplexed error robust fluorescence in situ hybridization (MERFISH) to map them spatially. We sampled [~]1 million cells across the dPnTg and defined the spatial distribution of over 120 neuronal subtypes. Our analysis identified an unpredicted high transcriptional diversity in this region and pinpointed many neuronal subtypes unique marker genes. We also demonstrated that many neuronal subtypes are transcriptionally similar between humans and mice, enhancing this studys translational value. Finally, we developed a freely accessible, GPU and CPU-powered dashboard (http://harvard.heavy.ai:6273/) that combines interactive visual analytics and hardware-accelerated SQL into a data science framework to allow the scientific community to query and gain insights into the data.

neuroscience↗

bioRxiv2023

Chronic stress triggers seeking of a starvation-like state in anxiety-prone female mice

Elevated anxiety often precedes anorexia nervosa and persists after weight restoration. Patients with anorexia nervosa often describe hunger as pleasant, potentially because food restriction can be anxiolytic. Here, we tested whether chronic stress can cause animals to prefer a starvation-like state. We developed a virtual reality place preference paradigm in which head-fixed mice can voluntarily seek a starvation-like state induced by optogenetic stimulation of hypothalamic agouti-related peptide (AgRP) neurons. Prior to stress induction, male but not female mice showed mild aversion to AgRP stimulation. Strikingly, following chronic stress, a subset of females developed a strong preference for AgRP stimulation that was predicted by high baseline anxiety. Such stress-induced changes in preference were reflected in changes in facial expressions during AgRP stimulation. Our study suggests that stress may cause females predisposed to anxiety to seek a starvation state, and provides a powerful experimental framework for investigating the underlying neural mechanisms.

neuroscience↗

bioRxiv2022

Sub-threshold neuronal activity and the dynamical regime of cerebral cortex

Cortical neurons exhibit temporally irregular spiking patterns and heterogeneous firing rates. These features arise in model circuits operating in a fluctuation-driven regime, in which fluctuations in membrane potentials emerge from the network dynamics. However, it is still unclear whether the cortex operates in this regime. We evaluated the fluctuation-driven hypothesis by analyzing spiking and sub-threshold membrane potentials of neurons in the sensory and frontal cortex recorded during a decision-making task. Standard fluctuation-driven models account for spiking statistics but fail to capture the heterogeneity in sub-threshold activity. We address this issue by effectively incorporating dendritic conductances into the standard models. Our model suggests that the frontal cortex operates in a fluctuation-driven regime. In contrast, excitatory neurons in layer 4 of the barrel cortex are not fluctuation-driven; they spike in response to occasional synchronous inputs. Our work reveals fundamental differences between cortical areas, suggesting that they operate in different dynamical regimes.

neuroscience↗

bioRxiv2022

Reconstruction and simulation of thalamoreticular microcircuitry

Thalamoreticular circuitry is known to play a key role in attention, cognition and the generation of sleep spindles, and is implicated in numerous brain disorders, but the cellular and synaptic mechanisms remain intractable. Therefore, we developed the first detailed computational model of mouse thalamus and thalamic reticular nucleus microcircuitry that captures morphological and biophysical properties of [~]14,000 neurons connected via [~]6M synapses, and recreates biological synaptic and gap junction connectivity. Simulations recapitulate multiple independent network-level experimental findings across different brain states, providing a novel unifying cellular and synaptic account of spontaneous and evoked activity in both wakefulness and sleep. Furthermore, we found that: 1.) inhibitory rebound produces frequency-selective enhancement of thalamic responses during wakefulness, in addition to its role in spindle generation; 2.) thalamic interactions generate the characteristic waxing and waning of spindle oscillations; and 3.) changes in thalamic excitability (e.g. due to neuromodulation) control spindle frequency and occurrence. The model is openly available and provides a new tool to interpret spindle oscillations and test hypotheses of thalamoreticular circuit function and dysfunction across different network states in health and disease.

neuroscience↗

bioRxiv2021

Visual association cortex links cues with conjunctions of reward and locomotor contexts

Postrhinal cortex (POR) and neighboring lateral visual association areas are necessary for identifying objects and interpreting them in specific contexts, but how POR neurons encode the same object across contexts remains unclear. Here, we imaged excitatory neurons in mouse POR across tens of days throughout initial cue-reward learning and reversal learning. As such, neurons were tracked across sessions/trials where the same cue was rewarded or unrewarded, during both locomotor and stationary contexts. Surprisingly, a large class of POR neurons were minimally cue-driven prior to learning. After learning, distinct clusters within this class responded selectively to a given cue when presented in a specific conjunction of reward and locomotion contexts. In addition, another class involved clusters of neurons whose cue responses were more transient, insensitive to reward learning, and adapted over thousands of presentations. These two classes of POR neurons may support context-dependent interpretation and context-independent identification of sensory cues.

neuroscience↗

bioRxiv2021

Realistic retinal modeling unravels the differential role of excitation and inhibition to starburst amacrine cells in direction selectivity

Retinal direction-selectivity originates in starburst amacrine cells (SACs), which display a centrifugal preference, responding with greater depolarization to a stimulus expanding from soma to dendrites than to a collapsing stimulus. Various mechanisms were hypothesized to underlie SAC centrifugal preference, but dissociating them is experimentally challenging and the mechanisms remain debatable. To address this issue, we developed the Retinal Stimulation Modeling Environment (RSME), a multifaceted data-driven retinal model that encompasses detailed neuronal morphology and biophysical properties, retina-tailored connectivity scheme and visual input. Using a genetic algorithm, we demonstrated that spatiotemporally diverse excitatory inputs - sustained in the proximal and transient in the distal processes - are sufficient to generate experimentally validated centrifugal preference in a single SAC. Reversing these input kinetics did not produce any centrifugal-preferring SAC. We then explored the contribution of SAC-SAC inhibitory connections in establishing the centrifugal preference. SAC inhibitory network enhanced the centrifugal preference, but failed to generate it in its absence. Embedding a direction selective ganglion cell (DSGC) in a SAC network showed that the known SAC-DSGC asymmetric connectivity by itself produces direction selectivity. Still, this selectivity is sharpened in a centrifugal-preferring SAC network. Finally, we use RSME to demonstrate the contribution of SAC-SAC inhibitory connections in mediating direction selectivity and recapitulate recent experimental findings. Thus, using RSME, we obtained a comprehensive mechanistic understanding of SACs centrifugal preference and its contribution to direction selectivity.

neuroscience↗

bioRxiv2021

The role of hub neurons in modulating cortical dynamics

Many neurodegenerative diseases are associated with the death of specific neuron types in particular brain regions. What makes the death of specific neuron types particularly harmful for the integrity and dynamics of the respective network is not well understood. To start addressing this question we used the most up-to-date biologically-realistic dense neocortical microcircuit (NMC) of rodent, which has reconstructed a volume of 0.3 mm3 and containing 31,000 neurons, 36 million synapses, and 55 morphological cell types arranged in 6 cortical layers. Using modern network science tools, we identified "hub-neurons" in the NMC, that are connected synaptically to a large number of their neighbors and systematically examined the impact of abolishing these cells. In general, the structural integrity of the network is robust to cells attack; yet, attacking hub neurons strongly impacted the "small worldness" topology of the network, whereas similar attacks on random neurons have a negligible effect. Such hub-specific attacks are also impactful on the network dynamics, both when the network is at its spontaneous synchronous state and when it was presented with synchronized thalamo-cortical visual-like input. We found that attacking layer 5 hub neurons are most harmful to the structural and functional integrity of the NMC. The significance of our results for understanding the role of specific neuron types and cortical layers for disease manifestation is discussed.

neuroscience↗

bioRxiv2020

Morphometric reconstructions atlas shows insult-driven plasticity in cortical VIP/ChAT interneurons

We developed an automatic morphometric reconstruction pipeline, Pop-Rec, and used it to study the morphologies of cortical cholinergic VIP/ChAT interneurons (VChIs). Cholinergic networks control high cognitive functions, but their local modulation and stress-driven plasticity patterns remained elusive. Reconstructing thousands of local VChIs registered to their exact coordinates in multiple cleared murine cortices highlighted distinct populations of bipolar and multipolar VChIs which differed in their dendritic spatial organization. Following mild unilateral whisker deprivation, Pop-Rec found both ipsi-and contra-lateral VChI dendritic arborization changes. Furthermore, RNA-seq of FACS-sorted VChIs showed differentially expressed dendritic, synapse and axon-modulating transcripts in whisker-deprived mice. Indicating novel steady-state morphological roles, those genes also clustered distinctly in naive single cell VChIs. This VChIs "morpheome" atlas is the first example of unbiased analysis of neuronal populations and holds the possibility to compare neuronal structure-function relationships across experimental conditions.

neuroscience↗

bioRxiv2020

Dense Computer Replica of Cortical Microcircuits Unravels Cellular Underpinnings of Auditory Surprise Response

The nervous system is notorious for its strong response evoked by a surprising sensory input, but the biophysical and anatomical underpinnings of this phenomenon are only partially understood. Here we utilized in-silico experiments of a biologically-detailed model of a neocortical microcircuit to study stimulus specific adaptation (SSA) in the auditory cortex, whereby the neuronal response adapts significantly for a repeated ("expected") tone but not for a rare ("surprise") tone. SSA experiments were mimicked by stimulating tonotopically-mapped thalamo-cortical afferents projecting to the microcircuit; the activity of these afferents was modeled based on our in-vivo recordings from individual thalamic neurons. The modeled microcircuit expressed naturally many experimentally-observed properties of SSA, suggesting that SSA is a general property of neocortical microcircuits. By systematically modulating circuit parameters, we found that key features of SSA depended on synergistic effects of synaptic depression, spike frequency adaptation and recurrent network connectivity. The relative contribution of each of these mechanisms in shaping SSA was explored, additional SSA-related experimental results were explained and new experiments for further studying SSA were suggested.

neuroscience↗

bioRxiv2020

A calcium-based plasticity model predicts long-term potentiation and depression in the neocortex

Long-term potentiation (LTP) and long-term depression (LTD) of pyramidal cell connections are among the key mechanisms underlying learning and memory in the brain. Despite their important role, only a few of these connections have been characterized in terms of LTP/LTD dynamics, such as the one between layer 5 thick-tufted pyramidal cells (L5-TTPCs). Comparing the available evidence on different pyramidal connection types reveals a large variability of experimental outcomes, possibly indicating the presence of connection-type-specific mechanisms. Here, we show that a calcium-based plasticity rule regulating L5-TTPC synapses holds also for several other pyramidal-to-pyramidal connections in a digital model of neocortical tissue. In particular, we show that synaptic physiology, cell morphology and innervation patterns jointly determine LTP/LTD dynamics without requiring a different model or parameter set for each connection type. We therefore propose that a similar set of plasticity mechanisms is shared by seemingly very different neocortical connections and that only a small number of targeted experiments is required for generating a complete map of synaptic plasticity dynamics in the neocortex.

neuroscience↗

bioRxiv2018

An efficient analytical reduction of nonlinear detailed neuron models

Detailed conductance-based nonlinear neuron models consisting of thousands of synapses are key for understanding of the computational properties of single neurons and large neuronal networks, and for interpreting experimental results. Simulations of these models are computationally expensive, considerably curtailing their utility. Neuron_Reduce is a new analytical approach to reduce the morphological complexity and computational time of nonlinear neuron models. Synapses and active membrane channels are mapped to the reduced model preserving their transfer impedance to the soma; synapses with identical transfer impedance are merged into one NEURON process still retaining their individual activation times. Neuron_Reduce accelerates the simulations by 40-250 folds for a variety of cell types and realistic number (10,000-100,000) of synapses while closely replicating voltage dynamics and specific dendritic computations. The reduced neuron-models will enable realistic simulations of neural networks at unprecedented scale, including networks emerging from micro-connectomics efforts and biologically-inspired \"deep networks\". Neuron_Reduce is publicly available and is straightforward to implement.

neuroscience↗

bioRxiv2018

Using subthreshold events to characterize the functional architecture of electrically coupled networks

The electrical connectivity in the inferior olive (IO) nucleus plays an important role in generating well-timed spiking activity. Here we combined electrophysiological and computational approaches to assess the functional organization of mice IO nucleus. Spontaneous fast and slow subthreshold events were commonly encountered during in vitro recordings. We show that the fast events represent a regenerative response in unique excitable spine-like structures in the axon hillock, whereas the slow events reflect the electrical connectivity between neurons ( spikelets). Recordings from cell pairs revealed the synchronized occurrence of distinct groups of spikelets; their rate and distribution enabled an accurate estimation of the number of connected cells and is suggestive of a clustered organization. This study thus provides a new perspective on the functional and structural organization of the olivary nucleus, insights into two different subthreshold non-synaptic events, and a novel experimental and theoretical approach to the study of electrically-coupled networks.

neuroscience↗